Setting Environment Variables for the Prime Third-Party Software and Databases

After you have installed the software, you may need to set environment variables to identify the location of the software, depending on where it is installed. For a default Schrödinger installation that uses web-based searching (does not use a local PDB or BLAST database), you should not need to set any environment variables, as all the software and the required databases are inside the installation. You only need to set environment variables if any of the software or databases is outside the Schrödinger installation. You can also use these environment variables if you have a customized copy of the databases, for example.

If the third-party products or databases that are outside the Schrödinger installation are in a single location, you can set SCHRODINGER_THIRDPARTY to this location. This location should have a database directory, in which databases are stored, and a bin directory, in which executables are stored. Each third-party product has its own subdirectory under these subdirectories. (The default location if this environment variable is not set is $SCHRODINGER/thirdparty.)
If some or all of third-party products or databases that are outside the Schrödinger installation are in different locations, you will need to set the environment variable for that product or database. The environment variables are listed in Table 1, with the locations that they should be set to. For example, if the PDB database is installed on a network drive, you would set the SCHRODINGER_PDB environment variable. This is useful if you already have copies of the databases or software that you want to use; however you must make sure that the software versions meet the requirements listed in Software Requirements for Prime.
If all of the third-party products and databases are installed into the default location in the Schrödinger software installation ($SCHRODINGER/thirdparty), including the PDB and BLAST databases, you do not need to set any extra environment variables. However, when you install a new Schrödinger software release, you must make sure that these PDB and BLAST databases are installed into the new default location. As the PDB and BLAST databases take up many GB of disk, installing them into the Schrödinger software installation is not recommended.

On Windows, if you are using an installed copy of the PDB to run Structure Prediction jobs, you must set the SCHRODINGER_PDB environment variable in Windows or UNC format. See for information on setting environment variables on Windows.

You can set the environment variables for remote hosts in the schrodinger.hosts file (see The Hosts File for more information). For use on a Linux host, you can set the environment variables for all users in /etc/profile.d.

Table 1. Environment variables defining the nonstandard location of third-party software and databases for Prime.
Environment Variable	Description
`SCHRODINGER_PDB`	PDB distribution directory (contains the `data` directory). Default: `$SCHRODINGER_THIRDPARTY/database/pdb`.
`PSP_BLASTDB`	BLAST database directory (contains directories `nr` and `pdb`). Default: `$SCHRODINGER_THIRDPARTY/database/blast`.
`PSP_BLAST_DIR`	BLAST executable directory. Default: `$SCHRODINGER_THIRDPARTY/bin/`platform`/blast/bin`.
`PSP_BLAST_DATA`	BLAST matrices directory. Default: `$SCHRODINGER_THIRDPARTY/bin/`platform`/blast/data`.
`PSP_HMMER_DIR`	HMMER installation directory (executables are in the `binaries` subdirectory). Default: `$SCHRODINGER_THIRDPARTY/bin/`platform`/hmmer`.
`PSP_HMMERDB`	Pfam database directory. Default: `$SCHRODINGER_THIRDPARTY/database/pfam`.
`PSP_PSIPRED_DIR`	PSIPRED installation (contains `bin` and `data` directories) Default: `$SCHRODINGER_THIRDPARTY/bin/`platform`/psipred`.
`PSP_PSIPRED_DB`	Sequence database to use for PSIPRED. Allowed values are `nr` and `pdb`. Default: `pdb`.
`PSP_SSPRO_DB`	Sequence database to use for SSPRO. Allowed values are `nr` and `pdb`. Default: `pdb`.